September 04, 2012

Progress in the Y-chromosome phylogeny

There is much of interest in the abstracts of the DNA in Forensics 2012 conference which will start very shortly, including news on the Tyrolean Iceman (he belonged to G-L91; and G2a "featured unexpectedly high densities within or near the Ötztal Alps."), speculations about a trans-Pacific spread of a lineage found in South Americans, and many other topics besides.

But, for me, the most interesting abstracts relate new developments in the Y-chromosome phylogeny world. The titles of the 3 abstracts are:

and, they all seem to be from authors working at The Wellcome Trust Sanger Institute.

Researchers used 1000Genomes low coverage data (2x) and high coverage Complete Genomics data to untangle the Y chromosome phylogeny. As expected, the 1000Genomes data weer of poorer quality, and had a large number (~14-17%) of false negatives, i.e., SNPs that were actually present in the samples were not discovered.

I list the main findings from the three abstracts:

The TMRCA of the entire tree was ~115 KYA (thousand years ago), and of the lineagesoutside Africa ~60 KYA, both as expected. Additional insights included a rapid expansion of hg F~40 KYA, and of R1b in Europe ~5-10 KYA. The archaeological counterpart of the former isunclear, but the latter is likely to represent a Neolithic expansion of this lineage

The GENETREE TMRCA for the complete set of chromosomes examined was 105-125KYA; times for the out-of-Africa movement were 62-79 KYA, a Paleolithic expansion 37-48KYA, and the expansion of R1b in Europe 7-10 KYA; rho times were broadly similar.

It confirmed Hg E (Bantu), O (China) and R1b (Europe) expansions associated with the Neolithic transitions in different parts of the world, and revealed that the expansion in Europe was the most extreme. One novel finding was a striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement, suggesting a previously unknown event of importance to male demography at this time.

I would say that these results are consistent with my "two deserts" theory and the climatic history of Africa and the Near East. Of course, I don't think there was a 60ky Out-of-Africa event, for a number of different reasons that I've written about to death. With respect to Y chromosome phylogeny, it is important to highlight one more time where I'm coming from:

The major African Y-haplogroup E belongs to the DE subclade of the CT clade:

I have color-coded the Eurasian lineages as "green", and the African ones as "red". Now, those who think that the age of CT corresponds to Out-of-Africa believe that this event was accompanied by a massive bottleneck which is responsible for the reduced genetic diversity of Eurasians compared to Africans.

But, the question is obvious: if there was such a massive bottleneck in Eurasian ancestors, then how come it is the Eurasians (the bottlenecked population) that ended up with most of the CT descendants?

There really is no archaeology to support a 62-79ky Out-of-Africa, the only archaeology (and anthropology) in support of Out-of-Africa relates to the pre-100ky period, with things like the Nubian complex, the Mt. Carmel hominins, Jebel Faya, and others links between Africa and the Near East.

There are no genetics to support it either: track every paper that has argued for ~60ky Out-of-Africa, and you will invariably find a 2.5x10-8/bp/generation or similar mutation rate and/or a recent human-chimp calibration hiding somewhere in the details. While the mutation wars rage, it is not certain how they will be resolved, but I would put money on the true mutation rate ending up much lower than the one dominating the literature, and, consequently, Out-of-Africa being much earlier.

Getting back to the topic, the "striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement" corresponds to the UP Revolution in west Eurasia. So, to recapitulate my thinking in bullet form:

70-50ky. Modern human biocultural evolution accelerates as they (i) face climate crisis, (ii) face new environments as they move out of North Africa-Arabia, (iii) face archaic humans in Eurasia and Africa. Haplogroup DE is group of "southern" Out-of-Arabians heading east (D) or west (E); Haplogroup CF is group of "northern" Out-of-Arabians, some of which head east (C) or stay around (F).

50-40ky. Culmination of the process leads to UP/LSA Revolution:

In East: some F descendants come to dominate over the early D and C settlers

In West Eurasia: other F descendants break through the Neandertal bottlecap and invade Europe with UP technologies

In Africa: E descendants (descended from DE back-migrants) kick-start the Lower Stone Age.

10 comments:

The spread of R1b in most of Europe seems to be very late neolithic (we have no sign of it before the Bronze Age), and so both dates in this paper are at least twice older than what we expect given current data.

Europe is the best studied place for ancient DNA, and these data appears to be at odds with what is already known for the region. Shouldn't this alone raise some red flags?

Either R1b had been lurking (and yet expanding) somewhere 7kya-10kya in much of Europe, even though we haven't seen it at all, or the estimates are all wrong and the dates possibly older than they should be.

In all of those cases, the expansion, the Neolithic expansion, was strictly speaking of sub-haplogroups of E, O and R1b respectively. Nobody disputes that Bantu expansion and Han Chinese expansion happened, or that those expansions had some demographic dimensions. Nobody disputes that a small subset of all types of E, O and R1b make up most of the total from this hgs in Africa, China and Western Europe respectively.

Absence of evidence is not evidence of absence. There have been arguments before that the R1b distribution in Europe is more or less completely separate from a similar "star" in Anatolia and therefor likely about equally old. My guess is that R1b spread with La Hoguette north, and then later just slightly more east when LBK separated into regional blocks. How and when it arrived in Southern France I don't know at this point, but some subbranches of R1b in Europe IMO show clear signs of very early neolithic expansion.

Terry,

I agree, several subgroups of O show clear signs of recent expansion with rice farmers. But as with R1b, this is not necessarily true for the original members of O nor for some of its subgroups.

"Nobody disputes that a small subset of all types of E, O and R1b make up most of the total from this hgs in Africa, China and Western Europe respectively".

Not really true in the case of O and China. Virtually all basal O3 haplogroups are found in the Han, although many would argue they have been co-opted into that group. Where O3 is found in non-Han a case can easily be made that its expansion merely pre-dates the Han expansion by a two or three thousand years, and represents an earlier Neolithic expansion than that of the Han. O1 is present in South China but its greatest expansion is probably associated with the Austronesians, which is undoubtedly a Neolithic expansion. O2 breaks into northern and southern branches, the southern appears related to the Late Hoabinhian. Also basically Neolithic.

"I agree, several subgroups of O show clear signs of recent expansion with rice farmers. But as with R1b, this is not necessarily true for the original members of O nor for some of its subgroups".

The 'Neolithic' in East Asia goes further back than just to 'rice farmers' though. But O3a2c looks very likely to have first expanded with rice farming. But the same may hold for O3a2 as a whole, and even for O3a1. O2's expansion is almost certainly pre-rice, but O1's may be associated with the expansion of rice through South China and SE Asia. and I do concede that the split between O1, O2 and O3, predates the Neolithic. twenty-seven thousand years is the date given in another recent paper on the subject.

"Haplogroup DE is group of 'southern' Out-of-Arabians heading east (D) or west (E)"

But it is difficult to make a case for D having moved east through South Asia. Many Y-DNA haplogroups survive in South Asia (both C-derived and F-derived) but the D haplogroups found there today (D1) obviously came from further east. It is unlikely that a single Y-DNA haplogroup would be the only one to suffer such extreme extinction through the expansion of later Y-DNAs.

Has not Otzi the Snowman had his complete Y-chromosome sequenced? Since his age is known, wouldn't comparison with modern G2a's allow the mutation rate to be read directly?

I was delighted to read the Francalacci paper, though I agree with you that "whether the current Sardinian population is descended from that initial expansion or from a later successful founder remains to be seen."

Prof. Francalacci pointed me to pages 7 and 24 of his paper's Supplement which addresses the matter of Otzi. He mentions difficulty reading the ancient sample, but concludes it to be consistent with his chronology.

Despite the reading difficulty, one can imagine an extrapolation to derive a mutation rate by comparison, but the paper makes no mention of such.

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